Bio::EnsEMBL::IdMapping MappingList
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Summary
Bio::EnsEMBL::IdMapping::MappingList - object holding a list of Entries
Package variables
No package variables defined.
Included modules
Bio::EnsEMBL::IdMapping::Serialisable
Bio::EnsEMBL::Utils::Exception qw ( throw warning )
Bio::EnsEMBL::Utils::ScriptUtils qw ( path_append )
Inherit
Bio::EnsEMBL::IdMapping::Serialisable
Synopsis
  # create a new MappingList
  my $mappings = Bio::EnsEMBL::IdMapping::MappingList->new(
    -DUMP_PATH  => $dump_path,
    -CACHE_FILE => 'gene_mappings.ser',
  );

  # add entries
  my $mappings->add_Entry($entry1);
  my $mappings->add_all( $entry2, $entry3 );

  # serialise to file
  $mappings->write_to_file;

  # later, read these mappings from file
  my $mappings1 = Bio::EnsEMBL::IdMapping::MappingList->new(
    -DUMP_PATH  => $dump_path,
    -CACHE_FILE => 'gene_mappings.ser',
  );
  $mappings1->read_from_file;
Description
This object represents a list of Bio::EnsEMBL::IdMapping::Entry
objects. It's essentially an OO wrapper for an array with some type
checking and convenience methods.
Methods
add_EntryDescriptionCode
add_allDescriptionCode
get_all_EntriesDescriptionCode
get_entry_countDescriptionCode
logDescriptionCode
newDescriptionCode
to_stringDescriptionCode
Methods description
add_Entrycode    nextTop
  Arg[1]      : Bio::EnsEMBL::IdMapping::Entry - Entry to add
  Example     : $mappings->add_Entry($entry);
  Description : Adds an Entry to the MappingList.
  Return type : none
  Exceptions  : thrown on wrong or missing argument
  Caller      : general
  Status      : At Risk
              : under development
add_allcodeprevnextTop
  Arg[1]      : List of Bio::EnsEMBL::IdMapping::Entry objects
  Example     : my @entries = ($entry1, $entry2);
                $mappings->add_all(@entries);
  Description : Adds a list of Entries to the MappingList.
  Return type : none
  Exceptions  : thrown on wrong argument
  Caller      : general
  Status      : At Risk
              : under development
get_all_EntriescodeprevnextTop
  Example     : foreach my $entry (@{ $mappings->get_all_Entries }) {
                  # do something with the entry
                }
  Description : Gets all Entries in the MappingList.
  Return type : Arrayref of Bio::EnsEMBL::IdMapping::Entry
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development
get_entry_countcodeprevnextTop
  Example     : my $num_entries = $mappings->get_entry_count;
  Description : Returns the number of Entries in the MappingList.
  Return type : Int
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development
logcodeprevnextTop
  Arg[1]      : String $type - object type (e.g. 'gene')
  Arg[2]      : String $dump_path - path for writing output
  Example     : $mappings->log('gene', $conf->param('basedir'));
  Description : Logs all Entries in the MappingList to a file. Used for
                debugging.
  Return type : none
  Exceptions  : thrown on I/0 error
  Caller      : general
  Status      : At Risk
              : under development
newcodeprevnextTop
  Arg[1-N]    : see superclass
  Example     : my $gene_mappings = Bio::EnsEMBL::IdMapping::MappingList->new(
                  -DUMP_PATH   => $dump_path,
                  -CACHE_FILE  => 'gene_mappings.ser',
                );
  Description : Constructor.
  Return type : Bio::EnsEMBL::IdMapping::MappingList
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development
to_stringcodeprevnextTop
  Example     : print LOG $mappings->to_string, "\n";
  Description : Returns a string representation of the MappingList. This is
                simply a multi-line string, where each line is a stringified
                Entry.
                Useful for debugging and logging.
  Return type : String
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development
Methods code
add_EntrydescriptionprevnextTop
sub add_Entry {
  my $self = shift;
  my $entry = shift;

  unless ($entry and $entry->isa('Bio::EnsEMBL::IdMapping::Entry')) {
    throw("Need a Bio::EnsEMBL::IdMapping::Entry");
  }

  push @{ $self->{'cache'}->{'entries'} }, $entry;
}
add_alldescriptionprevnextTop
sub add_all {
  my $self = shift;
  my @mappings = @_;

  foreach my $mapping (@mappings) {
    
    unless ($mapping->isa('Bio::EnsEMBL::IdMapping::MappingList')) {
      throw("Need a Bio::EnsEMBL::IdMapping::MappingList");
    }

    push @{ $self->{'cache'}->{'entries'} }, @{ $mapping->get_all_Entries };
  }
}
get_all_EntriesdescriptionprevnextTop
sub get_all_Entries {
  my $self = shift;
  return $self->{'cache'}->{'entries'};
}
get_entry_countdescriptionprevnextTop
sub get_entry_count {
  my $self = shift;
  return scalar(@{ $self->{'cache'}->{'entries'} });
}
logdescriptionprevnextTop
sub log {
  my $self = shift;
  my $type = shift;
  my $dump_path = shift;
  
  my $debug_path = path_append($dump_path, 'debug');
  my $logfile = "$debug_path/${type}_final_scores.txt";
  
  open(my $fh, '>', $logfile) or
    throw("Unable to open $logfile for writing: $!");

  foreach my $entry (@{ $self->get_all_Entries }) {
    print $fh ($entry->to_string."\n");
  }

  close($fh);
}
newdescriptionprevnextTop
sub new {
  my $caller = shift;
  my $class = ref($caller) || $caller;
  my $self = $class->SUPER::new(@_);

  # initialise internal datastructure unless we loaded a serialised object
  unless ($self->loaded) {
    $self->{'cache'}->{'entries'} = [];
  }

  return $self;
}
to_stringdescriptionprevnextTop
sub to_string {
  my $self = shift;
  
  my $string = '';
  
  foreach my $entry (@{ $self->get_all_Entries }) {
    $string .= $entry->to_string."\n";
  }

  return $string;
}


1;
}
General documentation
LICENSETop
  Copyright (c) 1999-2009 The European Bioinformatics Institute and
  Genome Research Limited.  All rights reserved.

  This software is distributed under a modified Apache license.
  For license details, please see

    /info/about/code_licence.html
CONTACTTop
  Please email comments or questions to the public Ensembl
  developers list at <ensembl-dev@ebi.ac.uk>.

  Questions may also be sent to the Ensembl help desk at
  <helpdesk@ensembl.org>.